Hello,

I am new here so please be kind :-)

Last summer my shower was having some problems with the caulk. I ripped it out and replaced with 100% silicone. Recently the caulking has become discolored underneath it. I don't know what I should do at this point. When in installed it I cleaned the area then dried it with a heatgun to make sure I didn't find more moisture.

Does this look like a deeper problem or does anyone have suggestions?

It will continue to do this but it's also not really a problem. A properly made tile shower pan will contain water within the mortar that it's made of. It's a common misconception that tile and grout are waterproof - they are not. While neither gets damaged by water both will let water pass through.

In your case, you have used a clear silicon to seal the joint between the shower floor and the walls, plus it looks like you also caulked into the corners of the wall tile. Putting caulk in these places is a good idea, as there is always a little expansion and contraction movement - especially between the floor and walls. But, don't use a clear silicon. Instead, use a silicon based grout caulk to match the color of your grout. As the purpose for putting the caulk in this area is to seal the cracks and make it easier to keep clean, the colored grout caulk will do the trick. Both the colored caulk and the clear will have water come up behind them, but the clear will be visible and will show the discoloration. The colored grout caulk will hide those sins.

So remove all the clear caulk, dry it out as best you can and replace it with a grout caulk. You'll still have to re-do this every couple of years but it will work fine and look much better.